use globalVariables to pass r-cmd-check when error given that there are undefined global variables; include devtools and here in description

Author: e-perl-NOAA

DESCRIPTION

@@ -51,7 +51,9 @@ Suggests:
     flextable,
     terra,
     rmarkdown,
-    tidyr
+    tidyr,
+    devtools,
+    here
 VignetteBuilder: 
     knitr
 VignetteDepends: 

R/cleanup_by_species.R

@@ -17,6 +17,7 @@
 #'
 #' @importFrom dplyr filter bind_rows
 #' @importFrom purrr map2 map
+#' @importFrom utils globalVariables
 #'
 #' @examples
 #' catch <- surveyresamplr::noaa_nwfsc_catch
@@ -174,3 +175,14 @@ join_dfs <- function(list_of_dfs, main_df, shared_column) {
   })
   return(merged_dfs)
 }
+
+# The following lines are used to declare global variables
+# to avoid "no visible binding for global variable" warnings in R CMD check.
+utils::globalVariables(
+  c(
+    "common_name",
+    "trawlid",
+    "latitude_dd",
+    "depth_m"
+  )
+)

R/plot_results.R

@@ -215,3 +215,16 @@ plot_results <- function(srvy, dir_out, dir_final = NULL) {
 
   return(out)
 }
+
+# The following lines are used to declare global variables
+# to avoid "no visible binding for global variable" warnings in R CMD check.
+utils::globalVariables(
+  c(
+    "depth_m",
+    "effort",
+    "log_est",
+    "se",
+    "est",
+    "year"
+  )
+)

R/wrapper_sdmtmb.R

@@ -60,3 +60,5 @@ wrapper_sdmtmb <- function(x, y, z, dir_spp, spp_info, n_knots = 300) {
 
   return(out)
 }
+
+utils::globalVariables("fit")

R/wrapper_surveyIndex.R

@@ -78,3 +78,5 @@ wrapper_surveyIndex <- function(x, y, z, dir_spp, spp_info, n_knots = 500) {
 
   return(out)
 }
+
+utils::globalVariables("fit")

R/wrapper_tinyVAST.R

@@ -78,3 +78,5 @@ wrapper_tinyVAST <- function(x, y, z, dir_spp, spp_info, n_knots = 500) {
 
   return(out)
 }
+
+utils::globalVariables("fit")